Preliminarily, here's the Query I would start with:

;WITH

cteMeasure As

(

SELECT m.[Patient_ID], m.[MEASUREMENT_DATETIME]

FROM [PROJECT].[dbo].[MEASURE] m

WHERE m.[TYPE] IN('SYSTOLIC', 'SYSLIE', 'SYSSTAND')

)

, lateTime As

(

SELECT p.[Patient_ID], max(m.[MEASUREMENT_DATETIME]) AS lateMeasure

FROM [PROJECT].[dbo].[PATIENT] p

INNER JOIN [PROJECT].[dbo].[CONSULTATIONS] c ON p.[Patient_ID] = c.[Patient_ID]

INNER JOIN cteMeasure m ON p.[Patient_ID] = m.[Patient_ID]

WHERE [VISIT_DATE] >= '2010-02-07'

AND m.[g_Site] = 'NSW_xxx_MC'

GROUP BY p.[Patient_ID]

HAVING COUNT(DISTINCT [VISIT_DATE]) >= 3

)

SELECT COUNT(UQ102.[Patient_ID])

FROM

(

SELECT me.[Patient_ID]

FROM cteMeasure me

JOIN lateTime

ON me.[Patient_ID] = lateTime.[Patient_ID]

AND me.[MEASUREMENT_DATETIME] = lateTime.[lateMeasure]

WHERE me.[MEASUREMENT] <> '' AND ISNUMERIC(me.[MEASUREMENT]) = 1

AND ( ( me.[MEASUREMENT] <> '0'

AND SUBSTRING(me.[MEASUREMENT], 1, 1) <> '0'

AND SUBSTRING(me.[MEASUREMENT], 1, 3) >= '100' AND SUBSTRING(me.[MEASUREMENT], 1, 3) < '250'

AND SUBSTRING(me.[MEASUREMENT], 2, 1) <> '.'

)

OR ( me.[MEASUREMENT] BETWEEN '0' AND '999'

AND SUBSTRING(me.[MEASUREMENT], 1, 2) > '70'

AND SUBSTRING(me.[MEASUREMENT], 2, 1) <> '.'

)

)

GROUP BY me.[Patient_ID]

) UQ102

It should be logically the same, so it may just produce the same query plan, but it has been simplified/reduced syntactically, so it's worht trying and seeing.